The animation used in Tangled v. Toy Story 3

So I watched Tangled for like the third time on thursday night and the animation still blows my mind. I found it shocking that it wasn't Pixar that created it but Walt Disney Animation Studios. The next day I watched Toy Story 3, which was created by Pixar Disney animation and it is obvious that the animation was different. I was wondering how the studio that produces the film effects how it is animated? Do they use totally different programs even though both are affiliated with Disney?